In 2002, a Federal Election Commission audit found a fund used by Weller for his re-election in 2000 received almost $110,000 that appeared to have violated federal campaign rules on the size and source of donations. Weller's fund returned all of the questioned contributions but did not admit deliberately violating any laws.[4][5]

On September 21, 2007, Weller announced that he would not seek another term, citing the need to spend more time with his family.[9]

Weller supported free trade when serving in Congress and traveled throughout Latin America and the Caribbean to build better relationships with public sector and business leaders. He was the number one supporter for the Panama trade agreement with the United States.[10]

Weller made efforts to eliminate the marriage penalty tax. He supported the use of tax incentives to help redevelop brownfield formal industrial land, developing a proposal with Democrats, such as Chicago Mayor Richard M. Daley, to do so.[4]

Weller voted again to raise the minimum wage in the 110th Congress.[13]

Weller sponsored a bill to expand concurrent receipt for wounded military veterans, but it did not pass.[14]

Weller promised prior to his marriage to GuatemalanCongresswomanZury Ríos Montt, that he would not vote on any legislation involving solely the U.S. and Guatemala. His advocacy and vote for CAFTA caused controversy however, despite it being a multi-nation agreement.[15] Weller has long supported free-trade agreements. As a FRG party leader, his wife is also a supporter of CAFTA.

Weller accepted money from two convicted associates of former congressman Duke Cunningham. Weller's spokesman said that the donations probably originated from his support of the research and development tax credit[16] and the money was donated to a charity in Oregon.[17] Weller is currently fighting a subpoena to testify in Cunningham's trial.[18]

On October 25, 2006, the Chicago Reader reported that Weller had disclosed three parcels of land he owned in Nicaragua on his financial disclosure forms: one purchased in 2002, one purchased in April 2004, and one purchased in December 2005. The newspaper also reported that it had obtained notarized bills of sale for three more lots owned by Weller that had never been listed on his forms: a lot sold in February 2005, a lot purchased in March 2005, and lot purchased in April 2005. The failure to properly disclosure property ownership is a violation of the Ethics in Government Act and the False Statements Accountability Act of 1996.

Weller's lawyer said that he couldn’t comment because of the attorney-client privilege.[24] Weller's campaign manager said Weller "does not own three more parcels in Nicaragua. He does not own six parcels in Nicaragua. He has filed his disclosure for everything that he owns."[25]

On September 7, 2007, the Chicago Tribune disclosed the results of their own investigation into his land deals, including discrepancies on declared prices and numbers of transactions, centered in the Playa Coco resort area. For example, Weller listed only one Nicaraguan property purchase on his 2005 disclosure form, but property records in Nicaragua showed that he bought or sold at least eight pieces of land.[26]